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Detailed information for vg0827152045:

Variant ID: vg0827152045 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 27152045
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCTAAGAATAAATCAGAACAAATATTTGCTTAGATTCATTGTAAAGAGAGATGAATTTCTTTTAGAACGGGGATGTAGCTAGCTAGGTTAGCTGTGTTC[G/A]
GACGCCCCTTTTCCCAACCACTCTTTTTTTTTTTCCGTGCGCACGTTTTTCAAACTACTAAACGGTGTATTTTTTAAAAAAAGTTTCTATACGAAAGTTG

Reverse complement sequence

CAACTTTCGTATAGAAACTTTTTTTAAAAAATACACCGTTTAGTAGTTTGAAAAACGTGCGCACGGAAAAAAAAAAAGAGTGGTTGGGAAAAGGGGCGTC[C/T]
GAACACAGCTAACCTAGCTAGCTACATCCCCGTTCTAAAAGAAATTCATCTCTCTTTACAATGAATCTAAGCAAATATTTGTTCTGATTTATTCTTAGAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.20%	1.30%	0.93%	2.62%	NA
All Indica	2759	95.40%	0.00%	0.18%	4.42%	NA
All Japonica	1512	93.40%	4.00%	2.51%	0.13%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	79.60%	0.00%	1.08%	19.35%	NA
Indica III	913	99.00%	0.00%	0.00%	0.99%	NA
Indica Intermediate	786	96.90%	0.10%	0.00%	2.93%	NA
Temperate Japonica	767	90.50%	5.50%	3.91%	0.13%	NA
Tropical Japonica	504	96.20%	2.60%	1.19%	0.00%	NA
Japonica Intermediate	241	96.70%	2.10%	0.83%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0827152045	G -> A	LOC_Os08g42960.1	upstream_gene_variant ; 4424.0bp to feature; MODIFIER	silent_mutation	Average:65.205; most accessible tissue: Callus, score: 83.348	N	N	N	N
vg0827152045	G -> A	LOC_Os08g42960.2	upstream_gene_variant ; 4818.0bp to feature; MODIFIER	silent_mutation	Average:65.205; most accessible tissue: Callus, score: 83.348	N	N	N	N
vg0827152045	G -> A	LOC_Os08g42950-LOC_Os08g42960	intergenic_region ; MODIFIER	silent_mutation	Average:65.205; most accessible tissue: Callus, score: 83.348	N	N	N	N
vg0827152045	G -> DEL	N	N	silent_mutation	Average:65.205; most accessible tissue: Callus, score: 83.348	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0827152045	4.02E-07	4.02E-07	mr1172_2	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251